A fuel cell system that includes a component for removing anionic contaminants is provided. The fuel system including a fuel cell stack, a fuel gas feed subsystem in communication with fuel cell anodes in the fuel cell stack, an oxygen-containing gas feed subsystem system in communication with fuel cell cathodes in the fuel cell stack, and an anionic scavenging subsystem in communication with the fuel gas feed subsystem and/or the an oxygen-containing gas feed subsystem.